Fig. 1

Characterization of developmentally regulated lncRNAs. a A scheme illustrating the cell types that were produced in this study by differentiation of hPSCs. Starting with undifferentiated cells at the top, hPSCs were differentiated to precursors of the germ layers, embryonic and extraembryonic progenitors, and terminally differentiated cells. The lineage and approximate developmental distance was estimated based on the expression of developmental markers as outlined below and in Additional file 1: Figure S1. In addition, primary preparations of keratinocytes, fibroblasts (adult and neonatal origin), and myotubes were analyzed. b–d RT-qPCR analysis of selected lineage markers corresponding to lateral mesoderm, and mesenchymal stem cells (b); definitive endoderm and lung progenitors (c); and neural progenitors and cortical neuron progenitors (d). Pluripotency genes OCT4, SOX2, and NANOG were analyzed in all samples. n = 2 independent experiments. e, f The absolute (e) and relative (f) expression of nuclear lncRNAs in undifferentiated human ESCs and germ layer and tissue progenitors as in b–d based on RT-qPCR analysis. n = 2 (CNP), 3 (LM, MSC), 4 (LP, pluripotent, NSC), 5 (DE) independent experiments, error bars represent standard deviation, p values were calculated by unpaired t-test; * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001. Cells at different passages were used for replicates. Abbreviations: LM: lateral mesoderm, MSC: mesenchymal stem cells, DE: definitive endoderm, LP: lung progenitors, CNP: cortical neuron progenitors, NSC: neural stem cells